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Earth, having recently found a Zero Point Module, sends reinforcements through the Stargate to defend Atlantis, meanwhile launching their newest ship, the Daedalus, to Atlantis to provide support. Soon, the Wraith fleet arrives to seize the city, launching waves of darts and beaming several soldiers down to the city, forcing the Expedition to launch an epic battle to stop the city from falling into the hands of the Wraith.

After considerable tinkering, McKay is able to link the new reactor to the weapons chair, and the platform is activated by Dr.Carson Beckett. McKay subsequently discovers that there are only a few dozen Drone weapons left. The remaining multi-thousand were used during the original siege 10,000 years previously. Without warning, there is an alarm; the Long range sensorss have detected hundreds of asteroids heading straight towards the proximity-activated nuclear bombs. McKay assesses that the rocks were launched by the Wraith, who have somehow discovered the mines. With no way to deactivate the warheads, the locater signals of all eight warheads vanish on the display as the mines detonate, with the Wraith at a safe distance. The radiation causes interference that disables the sensors.

Later, Everett meets with Sheppard in the Holo room and Sheppard grimly plays the history of the galaxy. Everett then informs him that he read the report Sheppard submitted surrounding the events in Rising. He explains that ColonelMarshall Sumner was a personal friend of his and that he is outraged with Sheppard for killing Sumner. Suddenly they are informed that there are approaching Wraith Darts and the battle for the city starts. Marines man the railguns and Sheppard takes the Chair; thanks to the Drone weapons and the railguns the first wave of Darts are destroyed but some parts of the city are hit.

Contemplating strategies, Sheppard suggests that they remotely control the Puddle Jumpers using the Chair and fly them, cloaked, into the hive ships armed with an explosive; he believes they should ask the Genii to use their nuclear weapons. Suddenly Teyla enters and informs them that there are Wraith in the city, who had invaded during the first wave. Together with a group of Athosians, the military starts to search for them. Meanwhile Weir gates to the Genii world, but is captured by them and held hostage. They want to exchange her for the C-4 they have been cheated out of, however Weir is able to convince them that they will use the C-4 only to test the devices, while they could be used for their true purpose of destroying the Wraith.

The Genii finally agree and supply the Atlantis team with two nuclear devices. The hunt for the Wraith is going badly, as the Wraith have begun damaging and destroying the Naqahdah generators powering the City.

Rodney and Zelenka working on the Genii bombs.

To make matters worse, McKay soon discovers that the Genii A-bombs are incomplete; he and Zelenka are soon in a lab completing the weapons against their fatigue, much to Beckett's disagreement.

At Atlantis the test-run of Sheppard's plan is a success, so McKay and Zelenka start to install the completed weapons into the Jumpers. Meanwhile, several men are taken out by the Wraith and the wounded are taken to the Alpha site. A second wave of Darts appears without warning; Sheppard mans the control chair to take control of the Jumpers. After several attempts at initializing the Chair, McKay realizes the reactor has depleted its supply of Naqahdah. Desperate, Sheppard decides to fly the Jumper himself in a hive ship, much to the shock of Weir.

As Weir cannot stop him, Sheppard rushes to the Jumper bay and takes it up. Outside, as Lt.Aiden Ford's team attempt to repel the Darts, a group of Wraith materializes in front of them. Inside, Everett's team is overrun and he is cornered by a Wraith. Out of ammo, the alien begins to feed off him. The final scene of season one sees Sheppard heading undetected into the Hive's Dart Bay, the nuke armed, while back in the control room, McKay counts down until detonation.

(The Atlantis base has just activated a self-destruct, only to have several personnel from Stargate Command arrive to help them)Everett: Good! Now does somebody want to please turn off that self-destruct?

(The Wraith have used asteroids to detonate several mines prematurely.)McKay: Your mines make one hell of a bang, Colonel, I'm sure the Wraith's ears are ringing.

McKay: I knew this was going to happen.Everett: Is that a fact?McKay: Yes, it's a fact! Look, you show up here with your guns and your brush cuts, but when it comes to actually saving the city, you turn to the scientists. And every time, what you ask is impossible.Everett: When was the last time you slept, Doctor?McKay: D-d-d-d…shut up, I have an idea

Ford: How about next time you can be the bait?Sheppard: Yeah, next time. Maybe...

(McKay is trying to get a reluctant Beckett to sit in the Ancient chair)McKay: It's out of drones; you couldn't do any damage if you wanted to, now SIT DOWN.

Beckett: You wanted to see me Rodney?McKay: Yes yes. I need something to keep me awake.Zelenka: Yeah, me too.Beckett: I've already given you something.McKay: (irritated) Yeah? Well we're building nuclear bombs here. Staying awake is sort of a prerequisite.Beckett: Snappy. All right. I'll get you another stimulant. Carry on. Zelenka: Thank you.

A deleted scene from this episode showed Sora Tyrus being returned to the Genii as part of their deal for the Genii A-bombs, but this was cut due to time constraints. Being cut, it is unclear if the event occurred or if Sora is still being held. It is likely canon as Sora reappears in the Stargate Atlantis: Legacy series where she mentions being released after three months.

While most of the events of the episode appear to take place over a day or so, in truth they appear to have occurred over the period of three to four days. At one point Weir mentions having asked a lot of everybody "the past few days" and the Daedalus appears at the beginning of "The Siege, Part 3" which starts immediately after the episode. Presumably, most of this time passed during the montage of everyone preparing for the Wraith attack before the first wave of Darts was sent.

This is the first appearance of the Mark II Naquadah generator, which is capable of a 600% power increase over Atlantis' Mark I reactors. It was designed to power the City's Weapons Chair.

During the episode, all of the Atlantis personnel are armed with guns, even the science personnel due to the threat. During the montage, they can be seen being given guns, presumably as a precaution in case they encounter the Wraith in the city.

While working on the Control Chair during the siege, McKay carries a FN P90 Personal Defense Weapon everywhere around the room with him and to Weir's office. This is only the second time McKay has been seen to be armed with a P90, the first being in "Suspicion" during Steve's capture.

It's possible, these expedition troops were considered a prototypal "United States Marine Space Corps".

In addition, Marine ColonelDillon Everett salutes Dr.Elizabeth Weir when relieving her. Marines do not salute when uncovered, and if under arms, are always covered. While it is impossible to tell if Everett is armed (presumably he is wearing a sidearm, but the scene does not show it), he should either not salute or be covered (wearing a cover) when he salutes.

From this scene it is not explicitly stated that the men wearing berets are Marines. In theory, the uniform could be one chosen by the SGC (a combined forces unit headed by an Air Force officer) and due to the nature of the unit, certain leeway given in standards of uniform wear by each service involved.

When McKay is told of the Deadalus being completed he says it is a sister ship to the Prometheus. This is incorrect the Deadalus is actually an entirely new class of ship.

However when McKay left Earth it was planned to be a 303 class ship not a 304.

When the second wave of Wraith Darts descend on the city, the Control chair had not yet been powered up, and it was established that all the Drone weapons were expended. However, during that scene you can see many drones flying up into the fray.

In this episode, we learn that the Life signs detector can not determine what type of life it detects. However, in the episode "Rising", we can clearly see Humans as white dots and Wraith as red dots.